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Characterize Disease-related Mutants of RAF Family Kinases by Using a Set of Practical and Feasible Methods
Published on: July 17, 2019
Computational study on the unbinding pathways of B-RAF inhibitors and its implication for the difference of residence
Yuzhen Niu1, Shuyan Li, Dabo Pan
1State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou 730000, China. xjyao@lzu.edu.cn.
Abstract:
B-RAF kinase is a clinically validated target implicated in melanoma and advanced renal cell carcinoma (RCC). PLX4720 and TAK-632 are promising inhibitors against B-RAF with different dissociation rate constants (k(off)), but the specific mechanism that determines the difference of their dissociation rates remains unclear. In order to understand the kinetically different behaviors of these two inhibitors, their unbinding pathways were explored by random acceleration and steered molecular dynamics simulations. The random acceleration molecular dynamics (RAMD) simulations show that PLX4720 dissociates along the ATP-channel, while TAK-632 dissociates along either the ATP-channel or the allosteric-channel. The steered molecular dynamics (SMD) simulations reveal that TAK-632 is more favorable to escape from the binding pocket through the ATP-channel rather than the allosteric-channel. The PMF calculations suggest that TAK-632 presents longer residence time, which is in qualitative agreement with the experimental k(off)(k(off) = 3.3 × 10(-2) s(-1) and ΔG(off) = -82.17 ± 0.29 kcal mol(-1) for PLX4720; k(off) = 1.9 × 10(-5) s(-1) and ΔG(off) = -39.73 ± 0.79 kcal mol(-1) for PLX4720). Furthermore, the binding free decomposition by MM/GBSA illustrates that the residues K36, E54, V57, L58, L120, I125, H127, G146 and D147 located around the allosteric binding pocket play important roles in determining the longer residence time of TAK-632 by forming stronger hydrogen bond and hydrophobic interactions. Our simulations provide valuable information to design selective B-RAF inhibitors with long residence time in the future.
Insights
Understanding BRAF inhibitor dissociation is key for cancer therapy. This study reveals TAK-632 has a longer residence time than PLX4720 due to distinct unbinding pathways and interactions, guiding future drug design.
Area of Science:
- Biochemistry
- Molecular Biology
- Pharmacology
Background:
- B-RAF kinase is a validated therapeutic target for melanoma and advanced renal cell carcinoma (RCC).
- PLX4720 and TAK-632 are B-RAF inhibitors with differing dissociation rates (koff).
- The mechanistic basis for these kinetic differences remains unclear.
Purpose of the Study:
- To elucidate the unbinding mechanisms and molecular determinants of differential dissociation rates between PLX4720 and TAK-632.
- To understand how these mechanisms influence inhibitor residence time.
- To provide insights for designing next-generation B-RAF inhibitors with improved efficacy.
Main Methods:
- Random Acceleration Molecular Dynamics (RAMD) simulations to explore unbinding pathways.
- Steered Molecular Dynamics (SMD) simulations to assess escape routes.
- Potential of Mean Force (PMF) calculations to estimate residence time.
- Molecular Mechanics with Generalized Born Surface Area (MM/GBSA) for binding free energy decomposition.
Main Results:
- PLX4720 primarily dissociates via the ATP channel.
- TAK-632 can utilize both ATP and allosteric channels for dissociation, with a preference for the ATP channel.
- TAK-632 exhibits a significantly longer residence time compared to PLX4720, consistent with experimental koff values.
- Specific residues (K36, E54, V57, L58, L120, I125, H127, G146, D147) near the allosteric site contribute to TAK-632's prolonged binding via enhanced interactions.
Conclusions:
- The distinct unbinding pathways and interactions dictate the differing residence times of PLX4720 and TAK-632.
- TAK-632's longer residence time is attributed to favorable interactions around the allosteric pocket.
- These findings offer valuable guidance for the rational design of selective B-RAF inhibitors with extended target engagement.
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